Depends what you're looking for. Fire Red Omega and Emerald 386 are hacks of Pokemon Fire Red and Emerald respectively, both of which include harder trainers and all 386 third-generation Pokemon.

Pokemon Fuligin is a hack very much like FireRed (it uses a lot of the same scripts FireRed uses) but with different maps, gyms, caves, etc.

Pokemon Shiny Gold X is a hard-version of Pokemon Gold (FireRed base) with a neat tileset if I recall correctly. Liquid Crystal is essentially the same thing but I believe it may be a bit easier. If you don't mind the lighter difficulty in Liquid Crystal, then you would enjoy the extra features it offers.

I've heard that the Ruby Destiny series is pretty hard, but I've never played it. It never seemed too appealing to me, but some people LOVE it. Snakewood is a Pokemon game based in Hoenn with new Pokemon though many, if not all, are based on original Pokemon. It has an undead theme, so the new Pokemon would be more gruesome than the Pokemon they are based off of.

Finally, check out the Emulation section on Pokecommunity.com, which is where most people go to get their ROM Hacks. You need an account to download ROMs off there. A blind run on a ROM hack is always fun. Games are only easy now that you know the gyms and what Pokemon are in what locations. This is usually what I do.

You could also try a monotype challenge, or make your own challenge (ie only use one Pokeball per route).